############################################################################## ############################################################################## ### ### Running command: ### ### /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD INSTALL alabaster.base ### ############################################################################## ############################################################################## * installing to library ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library’ * installing *source* package ‘alabaster.base’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ using C++17 g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I../inst/include -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/assorthead/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I../inst/include -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/assorthead/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -DR_NO_REMAP -c check_csv.cpp -o check_csv.o g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I../inst/include -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/assorthead/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -DR_NO_REMAP -c check_list.cpp -o check_list.o g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I../inst/include -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/assorthead/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -DR_NO_REMAP -c choose_numeric_missing_placeholder.cpp -o choose_numeric_missing_placeholder.o g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I../inst/include -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/assorthead/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -DR_NO_REMAP -c is_rfc3339.cpp -o is_rfc3339.o g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I../inst/include -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/assorthead/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -DR_NO_REMAP -c load_csv.cpp -o load_csv.o g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I../inst/include -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/assorthead/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -DR_NO_REMAP -c load_list.cpp -o load_list.o g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I../inst/include -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/assorthead/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -DR_NO_REMAP -c validate.cpp -o validate.o In file included from /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/assorthead/include/chihaya/validate.hpp:13, from /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/assorthead/include/chihaya/chihaya.hpp:10, from /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/assorthead/include/takane/utils_public.hpp:13, from /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/assorthead/include/takane/_validate.hpp:9, from /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/assorthead/include/takane/takane.hpp:4, from validate.cpp:2: /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/assorthead/include/chihaya/sparse_matrix.hpp: In function ‘void chihaya::sparse_matrix::internal::validate_indices(const H5::DataSet&, const std::vector&, size_t, size_t, bool) [with Index_ = long unsigned int]’: /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/assorthead/include/chihaya/sparse_matrix.hpp:51:32: warning: ‘previous’ may be used uninitialized [-Wmaybe-uninitialized] 51 | if (x > start && i <= previous) { | ~~^~~~~~~~~~~ /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/assorthead/include/chihaya/sparse_matrix.hpp:45:16: note: ‘previous’ was declared here 45 | Index_ previous; | ^~~~~~~~ /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/assorthead/include/chihaya/sparse_matrix.hpp: In function ‘void chihaya::sparse_matrix::internal::validate_indices(const H5::DataSet&, const std::vector&, size_t, size_t, bool) [with Index_ = int]’: /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/assorthead/include/chihaya/sparse_matrix.hpp:51:32: warning: ‘previous’ may be used uninitialized [-Wmaybe-uninitialized] 51 | if (x > start && i <= previous) { | ~~^~~~~~~~~~~ /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/assorthead/include/chihaya/sparse_matrix.hpp:45:16: note: ‘previous’ was declared here 45 | Index_ previous; | ^~~~~~~~ g++ -std=gnu++17 -shared -L/usr/local/lib -o alabaster.base.so RcppExports.o check_csv.o check_list.o choose_numeric_missing_placeholder.o is_rfc3339.o load_csv.o load_list.o validate.o /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Rhdf5lib/lib/libhdf5_cpp.a /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Rhdf5lib/lib/libhdf5.a -L/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Rhdf5lib/lib -lcrypto -lcurl -lsz -laec -lz -ldl -lm -lz installing to /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/00LOCK-alabaster.base/00new/alabaster.base/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (alabaster.base)